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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI ENOYL-ACYL CARRIER PROTEIN REDUCTASE IN COMPLEX WITH HYDROXYDIPHENYL ETHER COMPOUNDS, TRICLOSAN AND DICLOSAN
 
Authors :  H. H. Lee, J. H. Moon, S. W. Suh
Date :  31 Mar 07  (Deposition) - 17 Apr 07  (Release) - 24 Jun 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Antibacterial Target, Helicobacter Pylori, Type Ii Fatty Acid Biosynthesis, Enoyl-Acp-Reductase, Fabi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Lee, J. H. Moon, S. W. Suh
Crystal Structure Of The Helicobacter Pylori Enoyl-Acyl Carrier Protein Reductase In Complex With Hydroxydiphenyl Ether Compounds, Triclosan And Diclosan
Proteins V. 69 691 2007
PubMed-ID: 17879346  |  Reference-DOI: 10.1002/PROT.21586
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
    Chains: A, B, C, D
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: ENOYL-ACYL CARRIER PROTEIN REDUCTASE, NADH- DEPENDENT ENOYL-ACP REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2TCL4Ligand/IonTRICLOSAN

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , VAL A:14 , ALA A:15 , SER A:19 , ILE A:20 , LEU A:40 , LEU A:44 , LEU A:63 , ASP A:64 , VAL A:65 , VAL A:92 , ALA A:93 , ILE A:118 , LEU A:143 , SER A:144 , TYR A:145 , LYS A:162 , ALA A:188 , PRO A:190 , ILE A:191 , THR A:193 , ALA A:195 , TCL A:2414 , HOH A:2423BINDING SITE FOR RESIDUE NAD A 1780
2AC2SOFTWAREALA A:93 , PHE A:94 , ALA A:95 , TYR A:145 , TYR A:155 , ALA A:195 , ILE A:199 , PHE A:202 , NAD A:1780BINDING SITE FOR RESIDUE TCL A 2414
3AC3SOFTWAREGLY B:13 , VAL B:14 , ALA B:15 , SER B:19 , ILE B:20 , LEU B:40 , LEU B:44 , LEU B:63 , ASP B:64 , VAL B:65 , SER B:91 , VAL B:92 , ALA B:93 , ILE B:118 , LEU B:143 , SER B:144 , TYR B:145 , LYS B:162 , ALA B:188 , GLY B:189 , PRO B:190 , ILE B:191 , THR B:193 , ALA B:195 , TCL B:3414 , HOH B:3427 , HOH B:3435 , HOH B:3464BINDING SITE FOR RESIDUE NAD B 2780
4AC4SOFTWAREALA B:93 , ALA B:95 , LEU B:100 , TYR B:145 , TYR B:155 , ALA B:195 , NAD B:2780BINDING SITE FOR RESIDUE TCL B 3414
5AC5SOFTWAREGLY C:13 , VAL C:14 , ALA C:15 , SER C:19 , ILE C:20 , LEU C:40 , LEU C:44 , LEU C:63 , ASP C:64 , VAL C:65 , SER C:91 , VAL C:92 , ALA C:93 , ILE C:118 , LEU C:143 , SER C:144 , TYR C:145 , LYS C:162 , ALA C:188 , GLY C:189 , PRO C:190 , ILE C:191 , THR C:193 , LEU C:194 , ALA C:195 , TCL C:4414 , HOH C:4429 , HOH C:4444 , HOH C:4471BINDING SITE FOR RESIDUE NAD C 3780
6AC6SOFTWAREALA C:93 , PHE C:94 , ALA C:95 , LEU C:100 , TYR C:145 , TYR C:155 , ALA C:195 , NAD C:3780BINDING SITE FOR RESIDUE TCL C 4414
7AC7SOFTWAREGLY D:13 , VAL D:14 , ALA D:15 , SER D:19 , ILE D:20 , LEU D:40 , LEU D:44 , LEU D:63 , ASP D:64 , VAL D:65 , VAL D:92 , ALA D:93 , ILE D:118 , LEU D:143 , SER D:144 , TYR D:145 , LYS D:162 , ALA D:188 , GLY D:189 , PRO D:190 , ILE D:191 , THR D:193 , LEU D:194 , ALA D:195 , TCL D:5414 , HOH D:5425 , HOH D:5427 , HOH D:5434 , HOH D:5450BINDING SITE FOR RESIDUE NAD D 4780
8AC8SOFTWAREALA D:93 , ALA D:95 , LEU D:100 , TYR D:145 , TYR D:155 , MET D:158 , ALA D:195 , NAD D:4780BINDING SITE FOR RESIDUE TCL D 5414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PD3)

(-) Exons   (0, 0)

(no "Exon" information available for 2PD3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:274
 aligned with FABI_HELPY | O24990 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
           FABI_HELPY     2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
               SCOP domains d2pd3a_ A: Enoyl-ACP reductase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pd3A00 A:2-275 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh..eeeeee......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pd3 A   2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with FABI_HELPY | O24990 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
           FABI_HELPY     2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
               SCOP domains d2pd3b_ B: Enoyl-ACP reductase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pd3B00 B:2-275 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....eeeee..hhhhh.............hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pd3 B   2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain C from PDB  Type:PROTEIN  Length:274
 aligned with FABI_HELPY | O24990 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
           FABI_HELPY     2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
               SCOP domains d2pd3c_ C: Enoyl-ACP reductase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pd3C00 C:2-275 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.............hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pd3 C   2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain D from PDB  Type:PROTEIN  Length:274
 aligned with FABI_HELPY | O24990 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
           FABI_HELPY     2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
               SCOP domains d2pd3d_ D: Enoyl-ACP reductase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pd3D00 D:2-275 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -----------adh_short_C2-2pd3D01 D:13-251                                                                                                                                                                                                                  ------------------------ Pfam domains (1)
           Pfam domains (2) -----------adh_short_C2-2pd3D02 D:13-251                                                                                                                                                                                                                  ------------------------ Pfam domains (2)
           Pfam domains (3) -----------adh_short_C2-2pd3D03 D:13-251                                                                                                                                                                                                                  ------------------------ Pfam domains (3)
           Pfam domains (4) -----------adh_short_C2-2pd3D04 D:13-251                                                                                                                                                                                                                  ------------------------ Pfam domains (4)
         Sec.struct. author ......eeeee......hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh..eeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh...................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pd3 D   2 GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPIAQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (FABI_HELPY | O24990)
molecular function
    GO:0004318    enoyl-[acyl-carrier-protein] reductase (NADH) activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + NAD+ = trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0030497    fatty acid elongation    The elongation of a fatty acid chain by the sequential addition of two-carbon units.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

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 Related Entries

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        FABI_HELPY | O24990: 2pd4

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2pd4